Starting phenix.real_space_refine on Wed Sep 17 03:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbw_38231/09_2025/8xbw_38231.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 6 5.16 5 C 1573 2.51 5 N 501 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2671 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 1.02, per 1000 atoms: 0.38 Number of scatterers: 2671 At special positions: 0 Unit cell: (82.68, 71.02, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 36 15.00 O 555 8.00 N 501 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 75.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 454 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 73.6% alpha, 1.7% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.807A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.866A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 123 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 678 1.33 - 1.45: 614 1.45 - 1.57: 1412 1.57 - 1.69: 71 1.69 - 1.81: 9 Bond restraints: 2784 Sorted by residual: bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta sigma weight residual 1.536 1.578 -0.042 1.42e-02 4.96e+03 8.73e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG F 19 " pdb=" NH2 ARG F 19 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CZ ARG F 23 " pdb=" NH2 ARG F 23 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.28e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 3525 1.64 - 3.29: 311 3.29 - 4.93: 46 4.93 - 6.57: 8 6.57 - 8.22: 6 Bond angle restraints: 3896 Sorted by residual: angle pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 112.60 106.96 5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.97 121.08 -7.11 1.28e+00 6.10e-01 3.09e+01 angle pdb=" CA ASN F 25 " pdb=" C ASN F 25 " pdb=" N ILE F 26 " ideal model delta sigma weight residual 118.47 125.19 -6.72 1.26e+00 6.30e-01 2.85e+01 angle pdb=" C HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta sigma weight residual 109.51 117.73 -8.22 1.71e+00 3.42e-01 2.31e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.70 4.40 9.70e-01 1.06e+00 2.05e+01 ... (remaining 3891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1208 16.98 - 33.96: 184 33.96 - 50.94: 153 50.94 - 67.92: 64 67.92 - 84.90: 3 Dihedral angle restraints: 1612 sinusoidal: 911 harmonic: 701 Sorted by residual: dihedral pdb=" CA GLY L 32 " pdb=" C GLY L 32 " pdb=" N ILE L 33 " pdb=" CA ILE L 33 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N LYS F 20 " pdb=" CA LYS F 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C HIS E 39 " pdb=" N HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta harmonic sigma weight residual -122.60 -131.94 9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 1609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 424 0.102 - 0.204: 18 0.204 - 0.305: 1 0.305 - 0.407: 0 0.407 - 0.509: 1 Chirality restraints: 444 Sorted by residual: chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P DA I 51 " pdb=" OP1 DA I 51 " pdb=" OP2 DA I 51 " pdb=" O5' DA I 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.64 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 441 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 51 " -0.076 2.00e-02 2.50e+03 3.09e-02 2.62e+01 pdb=" N9 DA I 51 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 51 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 51 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 51 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DA I 51 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA I 51 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 51 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA I 51 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA I 51 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DA I 51 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 39 " -0.043 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS E 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS E 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 39 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 23 " 0.060 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO L 24 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 24 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 24 " 0.048 5.00e-02 4.00e+02 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 1 1.90 - 2.65: 54 2.65 - 3.40: 3563 3.40 - 4.15: 7271 4.15 - 4.90: 11510 Nonbonded interactions: 22399 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 90 " model vdw 1.155 3.120 nonbonded pdb=" NH2 ARG E 40 " pdb=" C2 DT J 90 " model vdw 2.155 3.340 nonbonded pdb=" O GLN L 23 " pdb=" N VAL L 49 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" NZ LYS L 73 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS L 57 " pdb=" OD1 ASP L 72 " model vdw 2.299 3.120 ... (remaining 22394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 2784 Z= 0.374 Angle : 1.060 8.216 3896 Z= 0.729 Chirality : 0.054 0.509 444 Planarity : 0.009 0.089 371 Dihedral : 23.744 84.903 1158 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.47), residues: 236 helix: -0.12 (0.36), residues: 159 sheet: None (None), residues: 0 loop : -0.82 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 27 TYR 0.016 0.002 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.025 0.004 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 2784) covalent geometry : angle 1.05980 ( 3896) hydrogen bonds : bond 0.15552 ( 168) hydrogen bonds : angle 5.49253 ( 453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9230 (m-30) cc_final: 0.9024 (p0) REVERT: L 73 LYS cc_start: 0.6764 (mttt) cc_final: 0.6410 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.5731 time to fit residues: 67.1664 Evaluate side-chains 74 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.080783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.055169 restraints weight = 10709.243| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.60 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 2784 Z= 0.222 Angle : 0.877 12.923 3896 Z= 0.473 Chirality : 0.044 0.188 444 Planarity : 0.006 0.043 371 Dihedral : 26.404 61.352 663 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 6.93 % Allowed : 31.68 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.51), residues: 236 helix: 0.29 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -1.64 (0.62), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 39 TYR 0.025 0.003 TYR E 99 PHE 0.014 0.003 PHE F 61 HIS 0.010 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 2784) covalent geometry : angle 0.87709 ( 3896) hydrogen bonds : bond 0.05788 ( 168) hydrogen bonds : angle 4.36861 ( 453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9449 (m-30) cc_final: 0.9219 (m-30) REVERT: E 104 PHE cc_start: 0.9503 (OUTLIER) cc_final: 0.9173 (t80) REVERT: E 110 CYS cc_start: 0.9157 (m) cc_final: 0.8933 (t) REVERT: E 120 MET cc_start: 0.7636 (mtt) cc_final: 0.7239 (mpp) REVERT: E 123 ASP cc_start: 0.8681 (m-30) cc_final: 0.7952 (m-30) outliers start: 14 outliers final: 6 residues processed: 93 average time/residue: 0.5231 time to fit residues: 49.8305 Evaluate side-chains 73 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.0060 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.078981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.057534 restraints weight = 11802.606| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.67 r_work: 0.3390 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2784 Z= 0.187 Angle : 0.883 11.261 3896 Z= 0.461 Chirality : 0.045 0.156 444 Planarity : 0.006 0.042 371 Dihedral : 25.857 68.213 663 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 5.94 % Allowed : 33.17 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.50), residues: 236 helix: -0.10 (0.38), residues: 174 sheet: None (None), residues: 0 loop : -2.06 (0.62), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.019 0.002 TYR E 99 PHE 0.028 0.003 PHE E 67 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2784) covalent geometry : angle 0.88286 ( 3896) hydrogen bonds : bond 0.05155 ( 168) hydrogen bonds : angle 4.28804 ( 453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9308 (m-30) cc_final: 0.8991 (p0) REVERT: E 104 PHE cc_start: 0.9550 (OUTLIER) cc_final: 0.9229 (t80) REVERT: E 110 CYS cc_start: 0.9391 (m) cc_final: 0.9044 (t) REVERT: E 120 MET cc_start: 0.7598 (mtt) cc_final: 0.7042 (mpp) REVERT: E 123 ASP cc_start: 0.8775 (m-30) cc_final: 0.7919 (m-30) REVERT: L 46 PHE cc_start: 0.5559 (m-80) cc_final: 0.5228 (m-80) REVERT: L 70 LYS cc_start: 0.7538 (mttt) cc_final: 0.7262 (tptp) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 0.4263 time to fit residues: 38.1982 Evaluate side-chains 75 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.073583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052345 restraints weight = 12293.711| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.32 r_work: 0.3281 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2784 Z= 0.243 Angle : 0.936 13.156 3896 Z= 0.487 Chirality : 0.047 0.222 444 Planarity : 0.006 0.038 371 Dihedral : 25.472 72.520 663 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 7.92 % Allowed : 34.65 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.48), residues: 236 helix: -0.24 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.44 (0.63), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 52 TYR 0.025 0.003 TYR E 99 PHE 0.051 0.004 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 2784) covalent geometry : angle 0.93580 ( 3896) hydrogen bonds : bond 0.05492 ( 168) hydrogen bonds : angle 4.28293 ( 453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9266 (m-30) cc_final: 0.9049 (p0) REVERT: E 82 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7588 (mt) REVERT: E 93 GLN cc_start: 0.8990 (pp30) cc_final: 0.8774 (pp30) REVERT: E 104 PHE cc_start: 0.9610 (OUTLIER) cc_final: 0.9395 (t80) REVERT: E 120 MET cc_start: 0.8111 (mtt) cc_final: 0.7634 (mpp) REVERT: F 63 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8759 (pp20) REVERT: F 92 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8106 (ttt180) REVERT: F 93 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7593 (tm-30) REVERT: L 46 PHE cc_start: 0.5546 (m-80) cc_final: 0.5337 (m-80) REVERT: L 77 GLU cc_start: 0.1847 (mt-10) cc_final: 0.1580 (mt-10) outliers start: 16 outliers final: 4 residues processed: 86 average time/residue: 0.4321 time to fit residues: 38.2426 Evaluate side-chains 72 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.074807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052767 restraints weight = 11500.747| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.62 r_work: 0.3249 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.9023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2784 Z= 0.187 Angle : 0.919 13.290 3896 Z= 0.469 Chirality : 0.046 0.209 444 Planarity : 0.005 0.037 371 Dihedral : 25.372 75.647 663 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.43 % Allowed : 41.09 % Favored : 51.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.48), residues: 236 helix: -0.33 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.57 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 63 TYR 0.014 0.001 TYR E 54 PHE 0.032 0.002 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2784) covalent geometry : angle 0.91870 ( 3896) hydrogen bonds : bond 0.04866 ( 168) hydrogen bonds : angle 4.39077 ( 453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 ILE cc_start: 0.9525 (pp) cc_final: 0.9324 (pp) REVERT: E 82 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8073 (mt) REVERT: E 90 MET cc_start: 0.9149 (mmm) cc_final: 0.8916 (mmm) REVERT: E 120 MET cc_start: 0.8136 (mtt) cc_final: 0.7851 (mpp) REVERT: F 47 SER cc_start: 0.5243 (OUTLIER) cc_final: 0.4799 (p) REVERT: F 52 GLU cc_start: 0.9281 (pm20) cc_final: 0.8954 (pm20) REVERT: F 92 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8155 (ttt180) REVERT: F 93 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7477 (tm-30) REVERT: L 43 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8456 (pp20) REVERT: L 46 PHE cc_start: 0.5720 (m-80) cc_final: 0.5487 (m-80) REVERT: L 50 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8372 (tp30) REVERT: L 70 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6779 (tptp) outliers start: 15 outliers final: 6 residues processed: 83 average time/residue: 0.5053 time to fit residues: 42.9625 Evaluate side-chains 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.0370 chunk 2 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.074774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052641 restraints weight = 11659.018| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.73 r_work: 0.3261 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.9438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 2784 Z= 0.187 Angle : 0.952 17.100 3896 Z= 0.486 Chirality : 0.047 0.254 444 Planarity : 0.005 0.041 371 Dihedral : 25.354 75.824 663 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 5.94 % Allowed : 44.06 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.48), residues: 236 helix: -0.36 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.38 (0.64), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 39 TYR 0.034 0.003 TYR E 99 PHE 0.034 0.003 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 2784) covalent geometry : angle 0.95212 ( 3896) hydrogen bonds : bond 0.05047 ( 168) hydrogen bonds : angle 4.49536 ( 453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8468 (ptp-110) REVERT: E 52 ARG cc_start: 0.8961 (pmm-80) cc_final: 0.8657 (pmm-80) REVERT: E 82 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (mt) REVERT: E 90 MET cc_start: 0.9175 (mmm) cc_final: 0.8916 (mmm) REVERT: E 104 PHE cc_start: 0.9498 (OUTLIER) cc_final: 0.9269 (t80) REVERT: E 120 MET cc_start: 0.8273 (mtt) cc_final: 0.7847 (mpp) REVERT: E 123 ASP cc_start: 0.8598 (m-30) cc_final: 0.8303 (m-30) REVERT: F 47 SER cc_start: 0.5049 (OUTLIER) cc_final: 0.4573 (p) REVERT: F 52 GLU cc_start: 0.9298 (pm20) cc_final: 0.8997 (pm20) REVERT: F 74 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8724 (mm-30) REVERT: F 92 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8111 (ttt180) REVERT: F 93 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7530 (tm-30) REVERT: L 43 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8358 (pp20) REVERT: L 50 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8433 (tp30) REVERT: L 70 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6721 (tptp) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 0.4745 time to fit residues: 39.9353 Evaluate side-chains 78 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.070233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049397 restraints weight = 12257.052| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.27 r_work: 0.3192 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 1.0291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2784 Z= 0.227 Angle : 1.014 15.513 3896 Z= 0.520 Chirality : 0.049 0.216 444 Planarity : 0.005 0.037 371 Dihedral : 25.312 78.642 663 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 7.43 % Allowed : 44.55 % Favored : 48.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.48), residues: 236 helix: -0.52 (0.37), residues: 167 sheet: None (None), residues: 0 loop : -1.33 (0.63), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.011 0.002 TYR E 99 PHE 0.028 0.002 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 2784) covalent geometry : angle 1.01411 ( 3896) hydrogen bonds : bond 0.05310 ( 168) hydrogen bonds : angle 4.68123 ( 453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9175 (ptm160) cc_final: 0.8592 (ptp-110) REVERT: E 52 ARG cc_start: 0.8964 (pmm-80) cc_final: 0.8711 (pmm-80) REVERT: E 70 LEU cc_start: 0.9368 (pp) cc_final: 0.9142 (pt) REVERT: E 90 MET cc_start: 0.9230 (mmm) cc_final: 0.9027 (mmm) REVERT: E 120 MET cc_start: 0.8483 (mtt) cc_final: 0.8117 (mpp) REVERT: F 46 ILE cc_start: 0.8779 (pt) cc_final: 0.8528 (pp) REVERT: F 47 SER cc_start: 0.5575 (OUTLIER) cc_final: 0.4926 (p) REVERT: F 52 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9064 (pm20) REVERT: F 60 VAL cc_start: 0.9425 (m) cc_final: 0.9050 (p) REVERT: F 63 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8708 (pp20) REVERT: F 92 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8313 (ttt180) REVERT: F 93 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7709 (tm-30) REVERT: L 46 PHE cc_start: 0.5165 (m-80) cc_final: 0.4945 (m-80) REVERT: L 50 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8702 (tp30) REVERT: L 60 LEU cc_start: 0.8860 (pp) cc_final: 0.8654 (pt) REVERT: L 70 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6966 (tptp) outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 0.4231 time to fit residues: 35.2211 Evaluate side-chains 82 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.073134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050855 restraints weight = 11725.909| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.69 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 1.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 2784 Z= 0.217 Angle : 1.019 14.550 3896 Z= 0.518 Chirality : 0.048 0.212 444 Planarity : 0.005 0.038 371 Dihedral : 25.324 80.589 663 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.94 % Allowed : 46.53 % Favored : 47.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.49), residues: 236 helix: -0.63 (0.37), residues: 167 sheet: None (None), residues: 0 loop : -1.53 (0.62), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.023 0.002 TYR F 88 PHE 0.025 0.003 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 2784) covalent geometry : angle 1.01897 ( 3896) hydrogen bonds : bond 0.05303 ( 168) hydrogen bonds : angle 4.63002 ( 453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 MET cc_start: 0.9000 (mmm) cc_final: 0.8085 (mmm) REVERT: E 120 MET cc_start: 0.8452 (mtt) cc_final: 0.8198 (mpp) REVERT: F 46 ILE cc_start: 0.8711 (pt) cc_final: 0.8456 (pp) REVERT: F 47 SER cc_start: 0.5606 (OUTLIER) cc_final: 0.5028 (p) REVERT: F 52 GLU cc_start: 0.9186 (pm20) cc_final: 0.8783 (pm20) REVERT: F 60 VAL cc_start: 0.9373 (m) cc_final: 0.8880 (p) REVERT: F 63 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8646 (pp20) REVERT: F 92 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8267 (ttt180) REVERT: F 93 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7694 (tm-30) REVERT: L 43 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8494 (pp20) REVERT: L 46 PHE cc_start: 0.5113 (m-80) cc_final: 0.4896 (m-80) REVERT: L 50 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8743 (mm-30) REVERT: L 60 LEU cc_start: 0.8850 (pp) cc_final: 0.8478 (pt) REVERT: L 70 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6895 (tptp) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.4088 time to fit residues: 35.8230 Evaluate side-chains 86 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 0.0570 chunk 21 optimal weight: 9.9990 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.072937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.051889 restraints weight = 12086.318| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.45 r_work: 0.3213 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 1.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2784 Z= 0.191 Angle : 1.084 16.145 3896 Z= 0.540 Chirality : 0.052 0.385 444 Planarity : 0.005 0.044 371 Dihedral : 25.328 80.107 663 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.46 % Allowed : 49.50 % Favored : 46.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.48), residues: 236 helix: -0.76 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.49 (0.63), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.011 0.001 TYR E 54 PHE 0.018 0.002 PHE F 61 HIS 0.002 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 2784) covalent geometry : angle 1.08431 ( 3896) hydrogen bonds : bond 0.05246 ( 168) hydrogen bonds : angle 4.71881 ( 453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8741 (mp) cc_final: 0.8109 (tm) REVERT: F 46 ILE cc_start: 0.8727 (pt) cc_final: 0.8444 (pp) REVERT: F 52 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: F 92 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8297 (ttt180) REVERT: F 93 GLN cc_start: 0.8585 (tm-30) cc_final: 0.7837 (tm-30) REVERT: L 43 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8511 (pp20) REVERT: L 47 HIS cc_start: 0.4871 (m90) cc_final: 0.4628 (m-70) REVERT: L 50 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8768 (tp30) REVERT: L 60 LEU cc_start: 0.8692 (pp) cc_final: 0.8413 (pt) REVERT: L 70 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7232 (tptp) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.3553 time to fit residues: 30.4378 Evaluate side-chains 81 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.072888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052190 restraints weight = 12039.861| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.43 r_work: 0.3225 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 1.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 2784 Z= 0.202 Angle : 1.158 17.656 3896 Z= 0.572 Chirality : 0.050 0.242 444 Planarity : 0.005 0.045 371 Dihedral : 25.241 78.967 663 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.46 % Allowed : 50.99 % Favored : 44.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.48), residues: 236 helix: -0.84 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.49 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 63 TYR 0.015 0.002 TYR F 88 PHE 0.019 0.002 PHE F 61 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 2784) covalent geometry : angle 1.15820 ( 3896) hydrogen bonds : bond 0.05302 ( 168) hydrogen bonds : angle 4.76957 ( 453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 57 SER cc_start: 0.8160 (p) cc_final: 0.7813 (p) REVERT: E 90 MET cc_start: 0.8988 (mmp) cc_final: 0.8552 (mmm) REVERT: F 46 ILE cc_start: 0.8805 (pt) cc_final: 0.8501 (pp) REVERT: F 52 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8788 (pm20) REVERT: F 66 ILE cc_start: 0.9711 (mp) cc_final: 0.9442 (pp) REVERT: F 92 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8330 (tmt170) REVERT: F 93 GLN cc_start: 0.8591 (tm-30) cc_final: 0.7832 (tm-30) REVERT: L 43 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8459 (pp20) REVERT: L 50 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8632 (tp30) REVERT: L 70 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7021 (tptp) REVERT: L 75 LEU cc_start: 0.8500 (mm) cc_final: 0.8202 (pp) outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.3354 time to fit residues: 28.0722 Evaluate side-chains 80 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.072443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.051655 restraints weight = 12126.723| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.43 r_work: 0.3228 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 1.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 2784 Z= 0.214 Angle : 1.184 16.814 3896 Z= 0.599 Chirality : 0.053 0.263 444 Planarity : 0.006 0.042 371 Dihedral : 25.210 79.406 663 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.96 % Allowed : 52.48 % Favored : 43.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.47), residues: 236 helix: -0.92 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -1.57 (0.62), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 52 TYR 0.012 0.001 TYR E 54 PHE 0.022 0.002 PHE F 61 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 2784) covalent geometry : angle 1.18402 ( 3896) hydrogen bonds : bond 0.05322 ( 168) hydrogen bonds : angle 4.86196 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.76 seconds wall clock time: 28 minutes 6.07 seconds (1686.07 seconds total)